Training in computational and bioinformatics approaches to biological problems is an important part of the mission of the Center for Biomedical Research Support. Each semester, we offer a variety of short courses each semester in diverse topics for learning computational approaches to solving biological problems. Courses are $50.00 unless noted otherwise. All meet for one day, lasting between two to four hours per course.

● Best Practices for 10X Single Cell Preparation (FREE!) (THIS COURSE IS FULL)

Cost: FREE but please register using the button below so we can assure there is enough space for everyone.

This course provides an introduction to the 10X Genomics Single Cell Controller and an overview of the assays offered by the GSAF (Genomic Sequencing and Analysis Facility). We will discuss NGS library preparation workflow and factors to consider in experimental design, with a focus on guidelines for preparing nuclei and cells from various sample types for use on the 10X instrument.

ABOUT THE INSTRUCTOR: Holly joined the Genomic Sequencing and Analysis Facility in 2017. She obtained her PhD in Genetics in 2006, with her graduate and postdoctoral studies focused on gene studies in cancer, followed by 5 years as a Biologist in a genomics core facility at the National Cancer Institute. She currently aids GSAF customers by preparing a variety of DNA/RNA libraries, assisting with Illumina sequencers, and operating the 10X Single Cell Controller.

This course provides an introduction to the bioinformatics analysis of single-cell RNA-seq (scRNA-seq) data, with a particular focus on methods especially appropriate for analysis of 10X Genomics data. Differences between bulk RNA-seq and scRNA-seq will be discussed in order to develop understanding of both what new methods are required versus what established RNA-seq analysis methods can be retained. Students interested in following along in class should bring their own laptops to the course with R (with Seurat, https://cran.r-project.org/web/packages/Seurat/index.html) installed.

ABOUT THE INSTRUCTOR: Dennis Wylie joined the CBRS Bioinformatics group in 2015. He has experience in NGS data analysis including variant calling and RNA-Seq-based biomarker discovery and predictive modeling (classification, regression, etc.). Prior to UT, he earned a PhD in Biophysics from UC Berkeley applying stochastic simulation methods to problems in immunology, did postdoctoral work modeling the transmission of infectious disease, and spent six years as a bioinformatician in industry.

Tag Seq is a method of sequencing the 3’ ends of mRNA in order to identify differential gene expression using a significantly cost effective method. This course is a introduction to this Tag Seq method as well as the bioinformatics involved in analyzing a Tag Seq dataset. We will discuss library prep, quality assessment, read mapping, gene quantification, differential expression analysis and downstream analysis. There are no prerequisites for taking this course.

ABOUT THE INSTRUCTOR: Dhivya Arasappan (Assistant Professor of Practice, Bioinformatics Consultant, CBRS)
Dhivya Arasappan has 9 years experience analyzing NGS data from multiple platforms: Illumina, PacBio and SOLiD. Her areas of expertise include: de novo genome assembly, particularly using hybrid sequencing data, RNA-Seq analysis, exome analysis, and benchmarking of bioinformatics tools. She is the research educator for the Big Data in Biology Freshman Research Initiative stream and teaches an RNA-Seq course as part of the Summer School for Big Data in Biology.

This course will cover advanced topics in writing Bash shell scripts, providing tips, examples and best practices for creating robust "pipeline scripts" that execute multiple processing steps. Topics include defining functions, argument processing and defaulting, error checking, effective use of awk, grep and sed, as well as subtleties of Unix stream and text manipulation.

ABOUT THE INSTRUCTOR: Anna Battenhouse is a research scientist in the lab of Dr. Edward Marcotte as well as leading the Biomedical Research Support Facility in its mission to support the IT and computational needs of the UT Austin biological sciences community. She has extensive experience writing pipeline scripts to process Next Generation Sequencing data and perform other functions.

PRE-REQUISITES: This is not an introductory course. Students must be comfortable performing basic tasks on the Linux command line. Suggested minimum background is completion of the "Intro to UNIX Command Line" short course and/or substantial command-line experience.
Students should bring their own laptops to the course, which will be used to access a shared computing environment. Windows users should install an SSH client such as Putty. Having a good text editor installed is also highly recommended. Good open source examples include Komodo Edit (Windows & Mac) and Notepad++ (Windows only).

●Overview of GSAF services (FREE!)

Cost: FREE but please register using the button below so we can assure there is enough space for everyone.

The course will provide an overview of the services the GSAF provides, the majority of the class will focus on NGS services, but briefly touch on a few others. This will include an introduction into the library prep services we offer; how each one is used and the submission requirements. A basic overview of each of the sequencing platforms along with an introduction of the various read length and run types you can choose from, followed by how to use our LIMS system for sample submission and track sample details on your job home page.

ABOUT THE INSTRUCTOR: Jessica Podnar joined the GSAF in 2010, prior to UT she worked for a small biotech company focused on drug discovery. She has been working in the field of molecular and cell biology for over 12 years and has been a part of the rapidly changing field of Next Generation Sequencing for most of her career. She is familiar with an assortment of library prep kits from multiple manufacturers to an array of custom library preps based on published methods. She can assist with almost any of your questions regarding NGS.

Learn the basics of using UNIX from the command line. Introductory topics include the filesystem, the shell, permissions, and text files. The course will touch on manipulating text files using standard UNIX utilities, how to string utilities together, and how to output the results to files. The goal of the course is to develop some basic comfort at the command line, get a sense of what's possible, and learn how to find help.

ABOUT THE INSTRUCTOR: Benni is a Bioinformatics Consultant in the CBRS. Python, Bash, and huge computing clusters are some of his favorite things. In a previous life Benni studied pure math, differential geometry in particular.

Students in the course will learn what a cluster is and how to use the world-class clusters available at the Texas Advanced Computing Center (TACC). The course will discuss the basic architecture of the Lonestar and Stampede computing clusters, how they compare to a regular computer, job launchers and job scheduling, and how to submit your own jobs to TACC. Custom tools by the Bioinformatics Consulting Group for job submission will be emphasized. Familiarity with a unix command line is a prerequisite. Students must also establish a TACC account and can do so by visiting this link..

ABOUT THE INSTRUCTOR: Benni is a Bioinformatics Consultant in the CBRS. Python, Bash, and huge computing clusters are some of his favorite things. In a previous life Benni studied pure math, differential geometry in particular.

PRE-REQUISITES: Familiarity and comfort with a Unix command line is a prerequisite